Retroelement-Linked Transcription Factor Binding Patterns Point to Quickly Developing Molecular Pathways in Human Evolution.
ChIP-seq
Human genome evolution
gene ontology
molecular pathways
omics approach in genetics
retrotransposons
transcription factor
Journal
Cells
ISSN: 2073-4409
Titre abrégé: Cells
Pays: Switzerland
ID NLM: 101600052
Informations de publication
Date de publication:
06 02 2019
06 02 2019
Historique:
received:
20
12
2018
revised:
29
01
2019
accepted:
30
01
2019
entrez:
10
2
2019
pubmed:
10
2
2019
medline:
10
2
2019
Statut:
epublish
Résumé
Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulation evolution. This approach allows for interrogating the regulatory evolution of organisms with RE-rich genomes. We aimed to characterize the evolution of transcriptional regulation for human genes and molecular pathways using RE-linked TFBS accumulation as a metric.
Sections du résumé
BACKGROUND
Retroelements (REs) are transposable elements occupying ~40% of the human genome that can regulate genes by providing transcription factor binding sites (TFBS). RE-linked TFBS profile can serve as a marker of gene transcriptional regulation evolution. This approach allows for interrogating the regulatory evolution of organisms with RE-rich genomes. We aimed to characterize the evolution of transcriptional regulation for human genes and molecular pathways using RE-linked TFBS accumulation as a metric.
Identifiants
pubmed: 30736359
pii: cells8020130
doi: 10.3390/cells8020130
pmc: PMC6406739
pii:
doi:
Substances chimiques
Retroelements
0
Transcription Factors
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Commentaires et corrections
Type : ErratumIn
Références
Front Immunol. 2018 Jan 30;9:30
pubmed: 29441061
Cell. 2012 May 11;149(4):740-52
pubmed: 22579280
N Engl J Med. 2017 Jul 27;377(4):361-370
pubmed: 28745987
Nat Rev Genet. 2009 Oct;10(10):691-703
pubmed: 19763152
Evodevo. 2015 Jan 29;6(1):3
pubmed: 25685316
Chem Rev. 2006 Feb;106(2):720-52
pubmed: 16464022
Nat Rev Genet. 2014 Apr;15(4):221-33
pubmed: 24590227
Biochim Biophys Acta. 2015 Aug;1849(8):1116-31
pubmed: 25934543
Science. 2007 Jun 8;316(5830):1497-502
pubmed: 17540862
Nucleic Acids Res. 2017 Jan 4;45(D1):D331-D338
pubmed: 27899567
Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32
pubmed: 26527727
Nat Rev Genet. 2016 Oct 14;17(11):704-714
pubmed: 27739533
Neuropharmacology. 2014 May;80:133-9
pubmed: 24389572
Am J Hum Genet. 2003 Apr;72(4):823-38
pubmed: 12632328
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S18
pubmed: 19534743
Hum Mutat. 2016 Sep;37(9):942-54
pubmed: 27319353
Cell. 1996 Nov 29;87(5):917-27
pubmed: 8945518
Cell Cycle. 2015;14(9):1476-84
pubmed: 25853282
Brief Funct Genomics. 2014 May;13(3):191-202
pubmed: 24335757
BMC Bioinformatics. 2009 Feb 03;10:48
pubmed: 19192299
Nat Protoc. 2009;4(1):44-57
pubmed: 19131956
Genet Sel Evol. 2016 Mar 31;48:27
pubmed: 27036106
Oncotarget. 2014 Oct 30;5(20):10198-205
pubmed: 25415353
Int J Biochem Cell Biol. 2009 Feb;41(2):285-97
pubmed: 18790074
Nat Rev Genet. 2008 May;9(5):397-405
pubmed: 18368054
Methods Mol Biol. 2017;1613:53-83
pubmed: 28849558
PLoS Comput Biol. 2007 Jul;3(7):e137
pubmed: 17630829
Science. 2016 Mar 4;351(6277):1083-7
pubmed: 26941318
Oncotarget. 2015 Oct 6;6(30):29347-56
pubmed: 26320181
Nat Genet. 2000 May;25(1):25-9
pubmed: 10802651
Philos Trans R Soc Lond B Biol Sci. 2013 Aug 12;368(1626):20120507
pubmed: 23938756
Nature. 2009 Jan 22;457(7228):413-20
pubmed: 19158787
Expert Opin Drug Discov. 2015 Jan;10(1):91-9
pubmed: 25306865
Cold Spring Harb Perspect Biol. 2010 Sep;2(9):a003483
pubmed: 20534711
Annu Rev Cell Dev Biol. 2015;31:399-428
pubmed: 26355593
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
N Engl J Med. 2009 Oct 8;361(15):1475-85
pubmed: 19812404
Front Chem. 2017 Jun 08;5:35
pubmed: 28642863
Cell Cycle. 2017 Oct 2;16(19):1810-1823
pubmed: 28825872
Biomed Res Int. 2016;2016:7861274
pubmed: 27957501
Nucleic Acids Res. 2009 Jan;37(1):1-13
pubmed: 19033363
Biochim Biophys Acta. 2014 Aug;1839(8):623-6
pubmed: 24412235
Genome Res. 2014 Dec;24(12):1963-76
pubmed: 25319995
Cell Mol Life Sci. 2015 Oct;72(19):3653-75
pubmed: 26082181
New Phytol. 2016 Apr;210(1):76-80
pubmed: 26137858
Cell Cycle. 2014;13(18):2847-52
pubmed: 25486472
Nat Rev Genet. 2008 May;9(5):411-2; author reply 414
pubmed: 18421312
Clin Oncol (R Coll Radiol). 2015 Oct;27(10):547-60
pubmed: 26282471
Nature. 2001 Feb 15;409(6822):860-921
pubmed: 11237011
Epigenetics. 2014 Nov;9(11):1485-95
pubmed: 25482055
Int J Evol Biol. 2014;2014:475981
pubmed: 24551476
Methods Mol Biol. 2017;1613:31-51
pubmed: 28849557
Nat Rev Genet. 2015 Apr;16(4):197-212
pubmed: 25707927
Trends Genet. 2016 Apr;32(4):238-249
pubmed: 26962025
Annu Rev Anim Biosci. 2014 Feb;2:259-83
pubmed: 25384143
Cell Mol Life Sci. 2015 Apr;72(8):1463-71
pubmed: 25548800